Welcome @amit_babu
Thanks for sharing the history and the error, very helpful!
So, both of the fasta files appear to have been Uploaded in an odd format – both are reporting as “binary” which usually means a problem with the datatype detection, or that possibly the wrong datatype was selected/assigned.
What to do
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Upload those two files again using all default settings, to allow Galaxy to “guess” the datatype. This can avoid mistyping. Getting Data into Galaxy
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Confirm that the datatype is fasta. If you get something else, you might want to uncompress the data and load it again. While fasta.gz might work with some tools, I’m not sure about this one (you could try, then fallback to fasta), and binary will definitely not work.
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Once all of the inputs are ready, try running Breaker3 again.
Please let us know if this works or if you need more help! 